AF3 ProteinDataset类的_patch方法解读
AlphaFold3 protein_dataset模块 ProteinDataset 类_patch 方法的主要目标是围绕锚点残基（anchor residues）裁剪蛋白质数据，提取一个局部补丁（patch）作为模型输入。源代码：
def _patch(self, data):
"""Cut the data around the anchor residues."""
# adapted from diffab
pos_alpha = data["X"][:, 2]
if self.mask_whole_chains:
mask_ = (data["mask"] * data["masked_res"]).bool()
anchor_points = pos_alpha.mean(0).unsqueeze(0)
anchor_ind = []
else:
anchor_ind = self.get_anchor_ind(data["masked_res"], data["mask"])
anchor_points = torch.stack( for ind in anchor_ind], dim=0)
dist_anchor = torch.cdist(pos_alpha, anchor_points, p=2).min(dim=1)# (L, )
dist_anchor[~data["mask"].bool()] = float("+inf")
initial_patch_idx = torch.topk(
dist_anchor,
k=min(self.initial_patch_size, dist_anchor.size(0)),
largest=False,
sorted=True,
)[
1
]# (initial_patch_size, )
patch_mask = data["masked_res"].bool().clone()
patch_mask[] = True
patch_mask = True
if self.sabdab:
antibody_mask = self._get_antibody_mask(data)
antigen_mask = ~antibody_mask
dist_anchor_antigen = dist_anchor.masked_fill(
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